4rws

Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target)

Method: X-RAY DIFFRACTION Dmax: 110.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

C-X-C chemokine receptor type 4/Endolysin chimeric protein

Enterobacteria phage T4

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1002–1161 Fragment:CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Mutation:L125W, T240P, D187C, C1054T, C1097T Viral macrophage inflammatory protein 2 × 1 (Q98157) X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5.5;293 K;100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K Resolution 3.10 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 238–397; UniProt 1002–1161

C-X-C chemokine receptor type 4/Endolysin chimeric protein

Enterobacteria phage T4

UniProt P61073

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–228 Chain A; UniProt 231–319 Fragment:CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Mutation:L125W, T240P, D187C, C1054T, C1097T Viral macrophage inflammatory protein 2 × 1 (Q98157) X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5.5;293 K;100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K Resolution 3.10 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CXCR4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–237; UniProt 2–228 Author chain A; PDBConstruct 401–489; UniProt 231–319

Viral macrophage inflammatory protein 2

Human herpesvirus 8 strain GK18

UniProt Q98157

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–94 Mutation:W5C C-X-C chemokine receptor type 4/Endolysin chimeric protein × 1 (P61073,P00720) X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5.5;293 K;100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K Resolution 3.10 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VMI2_HHV8P
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 24–94

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4rws

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rws
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rws
Deposition date deposition_date2014-12-05
Structure title titleCrystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target)
Keywords keywords;Human chemokine-chemokine receptor complex, GPCR signaling, PSI-Biology, GPCR network, membrane protein, GPCR, CXCR4, viral antagonist chemokine vMIP-II, membrane, lipidic cubic phase, T4L, Structural Genomics, SIGNALING PROTEIN, HYDROLASE ;; SIGNALING PROTEIN, HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.60
Radius of gyration Rg (electron density) rg_electron32.08
Forward intensity I(0) i045088900.00
Molecular weight molecular_weight56018.0 kDa
Excluded volume excluded_volume71411 ų
Envelope volume envelope_volume97123 ų
Hydration-shell volume shell_volume27235 ų
Envelope diameter envelope_diameter113.3
Shell Rg shell_rg36.03
Envelope Rg envelope_rg31.86
Shape Rg shape_rg32.06
Total Rg total_rg32.54
Total atoms total_atoms3953
Residues n_residues508
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.8
Rg (real space) rg_real32.97
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real4.5090e+07
I(0) uncertainty (real space) i0_real_error7.4800e+05
Rg (reciprocal space) rg_reciprocal32.82
I(0) (reciprocal space) i0_reciprocal45080000.0000
Solution quality estimate total_estimate0.8131
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.441
Kurtosis Kurtosis kurtosis-0.584
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6369000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.583; Smooth: 0.786

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4rwsc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.9 — IL8-like
Superfamily Superfamily superfamilyd.9.1 — Interleukin 8-like chemokines
Family Family familyd.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (1 domains)

Domain ID domain_id4rwsC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)